bioD:Gene: Difference between revisions

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|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]]
|{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]]
|{{Sub}}[[#Sequence Features|Sequence Features]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Genetic Interactions | Genetic Interactions]]
|{{Sub}}[[#Genetic Resources  |Genetic Resources]]
|{{Sub}}[[#Genetic Resources  |Genetic Resources]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
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{|{{Prettytable}}
{|   id="N46a9b87d665a2"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''bioD''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''bioD''
Biotin
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK0767, b0778, JW0761''<ref name='LIB:Riley_2006'/>, JW0761''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.12111.N46a9b87d665a2&page=12111&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK0767, b0778, JW0761''<ref name='LIB:Riley_2006'/>
|-
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='129533'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="W46a9b87dde08e"  class=" tableEdit Gene_location_table" 
|- {{table_heading_style}}
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!Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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MG1655
MG1655
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17.49 minutes&nbsp;
17.49 minutes&nbsp;
|
|
MG1655: 811493..812170<br />{{GBrowseFigureByCoord|810493|813170|ecoli|MG1655}}
MG1655: 811493..812170<br /><gbrowseImage>
name=NC_000913:811493..812170
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10120 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10120 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:810493..813170 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|810493|813170|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:811493..812170&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|811493|812170|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10120 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10120 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 804896..805573<br /><gbrowseImage>
name=NC_012967:804896..805573
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|804896|805573|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|804896|805573|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 714461..715138<br /><gbrowseImage>
name=NC_012759:714461..715138
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|714461|715138|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|714461|715138|FASTA Dump}}
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 812692..813369<br />{{GBrowseFigureByCoord|811692|814369|ecoli_W3110|W3110}}  
W3110: 812692..813369<br /><gbrowseImage>
name=NC_007779:812692..813369
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|811692|814369|GBrowse(W3110)}}  
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:811692..814369 GBrowse(W3110)]
{{GBrowseFastaLink|W3110|NC_007779|812692|813369|FASTA Dump}}
|-  
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:812692..813369&plugin_action=Go FASTA Dump]
[[DH10B]]
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DH10B: 865421..866098<br /><gbrowseImage>
name=NC_010473:865421..866098
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|864067|867452|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|864067|867452|FASTA Dump}}
 
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===Notes===
===Notes===
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|- {{table_heading_style}}
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
|-class='sortbottom'
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Coding Start (SO:0000323)
|
[[MG1655]]
|
811496
|
Edman degradation
|
PMID:8289297<br />
|
 
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====Notes====
====Notes====
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!Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-
|-
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bioDE13A,D
|
 
|
E13A,D
|
 
|
Almost no change in activity
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P13000 UniProt:P13000]
|-
|
bioDK16Q
|
 
|
K16Q
|
 
|
Complete loss of activity
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P13000 UniProt:P13000]
|-
|
bioDK38L,Q,R
|
 
|
K38L,Q,R
|
 
|
Complete loss of activity
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P13000 UniProt:P13000]
|-
|
bioDS42A,C
|
 
|
S42A,C
|
 
|
Almost no change in activity
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P13000 UniProt:P13000]
|-
|
bioDT12V
|
 
|
T12V
|
 
|
24000-fold increase in KM(ATP); little or no change in the Kd(ATP), KM(DAPA) and DTBS Kcat; essential role for this residue in the steady-state affinity for ATP
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P13000 UniProt:P13000]
|-  
|
|
&Delta;bioD (Keio:JW0761)
&Delta;bioD (Keio:JW0761)
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|
|
[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=106546 CGSC8320]<ref name='LIB:cgsc'/>  
|
|-
|
''bioD19''
|
 
|
 
|
 
|
 
|
 
|
[[cgscmutation:7573|CGSC:7573]]
|
|-
|
''bioD302''
|
 
|
 
|
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
 
|
 
|
 
|
[[cgscmutation:66558|CGSC:66558]]
|
|
   
   
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''&#916;bioD750::kan''
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:100200|CGSC:100200]]
|
 
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.12111.E4e04b8432df64-->
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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===Notes===


==Genetic Resources==
==Genetic Resources==
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!Resource!!Resource Type!!Source!!Notes/Reference
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JW0761
JW0761
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[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
|
[[PMID:16769691]]<ref name=PMID:16769691/>
PMID:16769691


Status:Clone OK
Status:Clone OK
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Primer 2:CCCAACAAGGCAAGGTTTATGTA  
Primer 2:CCCAACAAGGCAAGGTTTATGTA  
|-
|-
|
[[:Category:Kohara_Phage:4H7|4H7]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=201 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:3D4|3D4]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=202 Genobase]
|
PMID:3038334
|-  
|
|
[[nadA:Gene|nadA57::Tn10]]
[[nadA:Gene|nadA57::Tn10]]
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|
|
est. P1 cotransduction: 28% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 28% <ref name='LIB:Nichols_linked_Tn'/>  
|-
|-  
|
|
zbh-29::Tn10
zbh-29::Tn10
Line 203: Line 457:
CAG18493 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39400 CGSC7353]<ref name='LIB:cgsc'/>
CAG18493 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39400 CGSC7353]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 72% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 72% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zbi-29::Tn10


Synonyms:zbi-29::Tn10
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===Notes===
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-  
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10120 EcoCyc:EG10120] 
|
|-
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0118 EchoBASE:EB0118] 
EcoCyc:EG10120
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b0778 EcoliGenExpDB:b0778] 
EcoGene:EG10120
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C0858 ECOL199310CYC:C0858] 
RegulonDB:ECK120000116
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG10120 EcoGene:EG10120]
[http://www.ncbi.nlm.nih.gov/gene?term=945387 GeneID:945387]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=BIOD ECOO157CYC:BIOD] 
EchoBASE:EB0118
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
[[ASAP]]
|
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/956 CGSC:956] 
ASAP:ABE-0002650
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===Notes===
===Notes===
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===Categories===
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:MG1655]]
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[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:bio genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:33, 19 September 2013

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Nomenclature Location(s) and DNA Sequence Sequence Features Alleles and Phenotypes Genetic Interactions Genetic Resources Accessions Links References Suggestions

Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

bioD

Mnemonic

Biotin

Synonyms

ECK0767, b0778, JW0761[1], JW0761

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Notes

Location(s) and DNA Sequence

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See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain Map location Genome coordinates Genome browsers Sequence links

MG1655

17.49 minutes 

MG1655: 811493..812170
<gbrowseImage> name=NC_000913:811493..812170 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 804896..805573
<gbrowseImage> name=NC_012967:804896..805573 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 714461..715138
<gbrowseImage> name=NC_012759:714461..715138 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 812692..813369
<gbrowseImage> name=NC_007779:812692..813369 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 865421..866098
<gbrowseImage> name=NC_010473:865421..866098 source=DH10B preset=GeneLocation </gbrowseImage>

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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type Strain Genomic Location Evidence Reference Notes

Coding Start (SO:0000323)

MG1655

811496

Edman degradation

PMID:8289297[2]


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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele Nt change(s) AA change(s) Phenotype: Type Phenotype: Description Reference Availability Comments

bioDE13A,D

E13A,D

Almost no change in activity

seeded from UniProt:P13000

bioDK16Q

K16Q

Complete loss of activity

seeded from UniProt:P13000

bioDK38L,Q,R

K38L,Q,R

Complete loss of activity

seeded from UniProt:P13000

bioDS42A,C

S42A,C

Almost no change in activity

seeded from UniProt:P13000

bioDT12V

T12V

24000-fold increase in KM(ATP); little or no change in the Kd(ATP), KM(DAPA) and DTBS Kcat; essential role for this residue in the steady-state affinity for ATP

seeded from UniProt:P13000

ΔbioD (Keio:JW0761)

deletion

deletion

PMID:16738554[3]

Shigen
CGSC8320[4]

bioD19

CGSC:7573

bioD302

CGSC:66558

ΔbioD750::kan

PMID:16738554[3]

CGSC:100200


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Notes

Genetic Interactions

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Interactor Interaction Allele Score(s) Reference(s) Accessions Notes
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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource Resource Type Source Notes/Reference

JW0761

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCAGTAAACGTTATTTTGTCAC

Primer 2:CCCAACAAGGCAAGGTTTATGTA

4H7

Kohara Phage

Genobase

PMID:3038334[6]

3D4

Kohara Phage

Genobase

PMID:3038334[6]

nadA57::Tn10

Linked marker

CAG12147 = CGSC7351[4]

est. P1 cotransduction: 28% [7]

zbh-29::Tn10

Linked marker

CAG18493 = CGSC7353[4]

est. P1 cotransduction: 72% [7]
Synonyms:zbi-29::Tn10

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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc

EcoCyc:EG10120

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10120

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000116

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945387

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0118

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002650

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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<protect>

References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ Alexeev, D et al. (1994) Sequence and crystallization of Escherichia coli dethiobiotin synthetase, the penultimate enzyme of biotin biosynthesis. J. Mol. Biol. 235 774-6 PubMed
  3. ↑ 3.0 3.1 Baba, T et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2 2006.0008 PubMed
  4. ↑ 4.0 4.1 4.2 CGSC: The Coli Genetics Stock Center
  5. ↑ Kitagawa, M et al. (2005) Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K-12 ORF archive): unique resources for biological research. DNA Res. 12 291-9 PubMed
  6. ↑ 6.0 6.1 Kohara, Y et al. (1987) The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library. Cell 50 495-508 PubMed
  7. ↑ 7.0 7.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).

Categories

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